3.4 Microbial taxonomic composition and diversity measures
Amplicon sequencing of associated microbial communities on the Illumina
MiSeq produced a total of 2,653,026 raw reads, and after quality
filtering, dereplication and removal of non-bacterial sequences (Fig.
S7, supporting information), a total of 6,249 different ASVs were
identified. The dominant phyla detected across all samples were
Proteobacteria (60.4%) (Fig. 7). In all samples from Brazil and some
specimens from South Africa, Spain, and Australia, the phylum Firmicutes
was also abundant (18.7%). In contrast, Bacteroidetes (7.8%) and
Actinobacteria (5.5%) were observed only in some individuals across the
localities. Noteworthy, specimens from Brazil exhibited a higher
relative abundance of Firmicutes and Bacteroidetes than all other
locations (Fig. 7). At the family
level, Enterobacteriaceae (27.4%), Anaplasmataceae (4.4%), unclassified
Clostridiales (3.1%) and Acetobacteraceae (1.8%) were
predominant across all populations.
The individuals collected in South Africa and Brazil presented the
lowest and highest number, respectively, of unique bacterial ASVs (581
vs. 2,526) (Fig. S8A-C, Supporting information). South African
individuals shared a higher number of ASVs with the Palearctic and
Australasian locations (73 and 98 ASVs, respectively) than the
Neotropics (42 ASVs) (Fig. S8A-C, Supporting information). Individuals
from South Africa and Brazil were collected from the same host plant,
guava, but surprisingly the specimens collected from Brazil shared more
ASVs with its neighbouring country Colombia (89 ASVs), despite being
collected from different host plants, than with their putative native
region in South Africa (52 ASVs) (Fig. S8B, Supporting information).
This suggests that the bacterial composition remained similar to the
native source in some localities, despite the medflies being collected
from different host plants and geographically distant areas (see Fig. 1
and Supplementary Table 1).
Based on Shannon and Inverse Simpson diversity indexes, samples
collected in South Africa appeared to have the lowest microbial
diversity. At the same time, flies collected from different host plants
and geographically distant sampling sites such as Israel, Spain and
Australia showed the lowest disparity in diversity indexes, suggesting a
similarity in microbial diversity. Conversely, the Neotropical region
tended to have a more diverse microbiome, and samples from Brazil
presented the highest diversity indexes (Fig. S9, Supporting
information).